@@ -2,7 +2,7 @@ Package: Rgraphviz

 Title: Provides plotting capabilities for R graph objects

 Description: Interfaces R with the AT and T graphviz library for

         plotting R graph objects from the graph package.

-Version: 2.7.0

+Version: 2.7.1

 Author: Jeff Gentry, Li Long, Robert Gentleman, Seth Falcon,

    Florian Hahne, Deepayan Sarkar, Kasper Daniel Hansen

 Maintainer: Kasper Daniel Hansen <khansen@jhsph.edu>

@@ -2,6 +2,13 @@

 \title{Rgraphviz News}

 \encoding{UTF-8}

+\section{Version 2.7.x}{

+  \itemize{

+    \item Fixed include statements in Graphviz code.

+  }

+}

+

+

 \section{Version 2.5.x}{

   \itemize{

     \item Expose mai argument in plot,Ragraph-method.

new file mode 100755

@@ -0,0 +1,21 @@

+#!/bin/bash -e

+

+## Find all #include <XX>

+grep -R "#include <" * > all_includes.txt

+

+## Clean, and sort the include statements, so only the header remains

+cut -f2 -d: all_includes.txt | sort | uniq | sed 's:.*#include <::' | sed 's:\.h>.*:.h:' | grep -v ">$" | grep -v "all_includes.txt" | sort -b > all_include_statements.txt

+

+## Find all header files

+find . -iname "*.h" | sed 's:.*/::' | sort | uniq | sort -b > all_header_files.txt

+

+## Find intersection between header files and #include <XX>; these needs to be fixed

+join all_include_statements.txt all_header_files.txt > need_fixes.txt

+

+cat need_fixes.txt | while read include

+do

+  FIXFILES=`grep -R -l "#include <$include>" * | grep -v all_include`

+  sed -i "_tmp" "s:#include <$include>:#include \"$include\":" $FIXFILES

+done

+

+    

@@ -43,3 +43,9 @@ cd graphviz-2.28.0

 patch -p1 < ../patches_2.28.0/graphviz-2.28.0-configure.patch

 autoreconf

 cd ..

+

+echo 'Fixing #include < to be #include "'

+cp find_includes.sh ../../src/graphviz/lib

+cd ../../src/graphviz/lib

+./find_includes.sh

+

@@ -23,7 +23,7 @@

 ..

 .ta 1.0i 2.0i 3.0i 4.0i 5.0i

 .Cs

-#include <cdt.h>

+#include "cdt.h"

 .Ce

 .Ss "DICTIONARY TYPES"

 .Cs

@@ -18,7 +18,7 @@ extern "C" {

 #ifndef BLOCKPATH_H

 #define BLOCKPATH_H

-#include <circular.h>

+#include "circular.h"

     extern nodelist_t *layout_block(Agraph_t * g, block_t * sn, double);

     extern int cmpNodeDegree(Dt_t *, Agnode_t **, Agnode_t **, Dtdisc_t *);

@@ -18,8 +18,8 @@ extern "C" {

 #ifndef BLOCKTREE_H

 #define BLOCKTREE_H

-#include <render.h>

-#include <circular.h>

+#include "render.h"

+#include "circular.h"

     extern block_t *createBlocktree(Agraph_t * g, circ_state * state);

     extern void freeBlocktree(block_t *);

@@ -18,8 +18,8 @@ extern "C" {

 #ifndef CIRCPOS_H

 #define CIRCPOS_H

-#include <render.h>

-#include <circular.h>

+#include "render.h"

+#include "circular.h"

     extern void circPos(Agraph_t * g, block_t * sn, circ_state *);

@@ -124,7 +124,7 @@ typedef struct {

 #define DEGREE(n) (ND_order(n))

-#include <circo.h>

+#include "circo.h"

 #ifdef __cplusplus

 extern "C" {

@@ -12,9 +12,9 @@

  *************************************************************************/

-#include <deglist.h>

-#include <circular.h>

-#include <blockpath.h>

+#include "deglist.h"

+#include "circular.h"

+#include "blockpath.h"

 #include <assert.h>

 typedef struct {

@@ -12,7 +12,7 @@

  *************************************************************************/

-#include <nodeset.h>

+#include "nodeset.h"

 static nsitem_t *mkItem(Dt_t * d, nsitem_t * obj, Dtdisc_t * disc)

@@ -18,7 +18,7 @@ extern "C" {

 #ifndef HTMLLEX_H

 #define HTMLLEX_H

-#include <agxbuf.h>

+#include "agxbuf.h"

     extern int initHTMLlexer(char *, agxbuf *, int);

     extern int htmllex(void);

@@ -14,8 +14,8 @@

 #ifndef _POINTSET_H

 #define _POINTSET_H 1

-#include <cdt.h>

-#include <geom.h>

+#include "cdt.h"

+#include "geom.h"

 #ifdef __cplusplus

 extern "C" {

@@ -19,7 +19,7 @@

 #include "dot.h"

 #ifdef ORTHO

-#include <ortho.h>

+#include "ortho.h"

 #endif

 #define	NSUB	9		/* number of subdivisions, re-aiming splines */

@@ -25,9 +25,9 @@

 #include <config.h>

 #endif

-#include <clusteredges.h>

-#include <fdp.h>

-#include <neatoprocs.h>

+#include "clusteredges.h"

+#include "fdp.h"

+#include "neatoprocs.h"

 #include "vispath.h"

 typedef struct {

@@ -18,8 +18,8 @@ extern "C" {

 #ifndef CLUSTEREDGES_H

 #define CLUSTEREDGES_H

-#include <render.h>

-#include <adjust.h>

+#include "render.h"

+#include "adjust.h"

     extern int compoundEdges(graph_t * g, expand_t* pm, int splines);

@@ -23,9 +23,9 @@

 /* use PRIVATE interface */

 #define FDP_PRIVATE 1

-#include <fdp.h>

-#include <comp.h>

-#include <pack.h>

+#include "fdp.h"

+#include "comp.h"

+#include "pack.h"

 #include <assert.h>

 #define MARK(n) (marks[ND_id(n)])

@@ -18,7 +18,7 @@ extern "C" {

 #ifndef COMP_H

 #define COMP_H

-#include <render.h>

+#include "render.h"

     extern graph_t **findCComp(graph_t *, int *, int *);

@@ -21,9 +21,9 @@

 #define FDP_PRIVATE

-#include <dbg.h>

-#include <neatoprocs.h>

-#include <fdp.h>

+#include "dbg.h"

+#include "neatoprocs.h"

+#include "fdp.h"

 #include <math.h>

 static int indent = -1;

@@ -20,9 +20,9 @@ extern "C" {

 #ifdef DEBUG

-#include <fdp.h>

+#include "fdp.h"

 #include <stdio.h>

-#include <graph.h>

+#include "graph.h"

     extern double Scale;

     extern void outputGraph(Agraph_t *, FILE *, int);

@@ -14,7 +14,7 @@

 #ifndef FDP_H

 #define FDP_H

-#include <render.h>

+#include "render.h"

 #ifdef FDP_PRIVATE

@@ -24,9 +24,9 @@

 /* uses PRIVATE interface for NOTUSED */

 #define FDP_PRIVATE 1

-#include <fdp.h>

-#include <grid.h>

-#include <macros.h>

+#include "fdp.h"

+#include "grid.h"

+#include "macros.h"

   /* structure for maintaining a free list of cells */

 typedef struct _block {

@@ -22,8 +22,8 @@ extern "C" {

 #include <config.h>

 #endif

-#include <render.h>

-#include <cdt.h>

+#include "render.h"

+#include "cdt.h"

     typedef struct _grid Grid;

@@ -43,9 +43,9 @@

 #include <unistd.h>

 #endif

 #include <ctype.h>

-#include <dbg.h>

-#include <grid.h>

-#include <neato.h>

+#include "dbg.h"

+#include "grid.h"

+#include "neato.h"

 #ifndef HAVE_SRAND48

 #define srand48 srand

@@ -27,9 +27,9 @@ Increase less between tries

 /* uses PRIVATE interface */

 #define FDP_PRIVATE 1

-#include <xlayout.h>

-#include <adjust.h>

-#include <dbg.h>

+#include "xlayout.h"

+#include "adjust.h"

+#include "dbg.h"

 #include <ctype.h>

 /* Use bbox based force function */

@@ -18,7 +18,7 @@ extern "C" {

 #ifndef XLAYOUT_H

 #define XLAYOUT_H

-#include <fdp.h>

+#include "fdp.h"

     typedef struct {

 	int numIters;

@@ -15,7 +15,7 @@

 #include <stdio.h>

 #include <stdlib.h>

 #include <string.h>

-#include <agxbuf.h>

+#include "agxbuf.h"

 #define N_GNEW(n,t)	 (t*)malloc((n)*sizeof(t))

@@ -11,7 +11,7 @@

  * Contributors: See CVS logs. Details at http://www.graphviz.org/

  *************************************************************************/

-#include <digcola.h>

+#include "digcola.h"

 #ifdef DIGCOLA

 #include "kkutils.h"

@@ -47,7 +47,7 @@

 #include "matrix_ops.h"

 #include "kkutils.h"

 #include "conjgrad.h"

-#include <csolve_VPSC.h>

+#include "csolve_VPSC.h"

 #include "quad_prog_vpsc.h"

 #include "quad_prog_solver.h"

 #include "matrix_ops.h"

@@ -18,7 +18,7 @@ extern "C" {

 #ifndef DIGCOLA_H

 #define DIGCOLA_H

-#include <defs.h>

+#include "defs.h"

 #ifdef DIGCOLA

 extern void compute_y_coords(vtx_data*, int, double*, int);

 extern double compute_hierarchy(vtx_data*, int, double, double, 

@@ -35,7 +35,7 @@ extern "C" {

 		      double **(&new_coords));

 #else

-#include <defs.h>

+#include "defs.h"

     extern void embed_graph(vtx_data * graph, int n, int dim, DistType ***,

 			    int);

@@ -11,7 +11,7 @@

  * Contributors: See CVS logs. Details at http://www.graphviz.org/

  *************************************************************************/

-#include <memory.h>

+#include "memory.h"

 #include <stdio.h>

 /* Priority queue:

@@ -46,7 +46,7 @@

  */

 #include <math.h>

-#include <neato.h>

+#include "neato.h"

 static double *scales;

 static double **lu;

@@ -23,7 +23,7 @@

 #include <mosek.h> /* Include the MOSEK definition file. */

 #include "types.h"

-#include <csolve_VPSC.h>

+#include "csolve_VPSC.h"

 typedef struct {

 	int r;

@@ -11,9 +11,9 @@

  * Contributors: See CVS logs. Details at http://www.graphviz.org/

  *************************************************************************/

-#include <multispline.h>

-#include <delaunay.h>

-#include <neatoprocs.h>

+#include "multispline.h"

+#include "delaunay.h"

+#include "neatoprocs.h"

 #include <math.h>

@@ -1238,7 +1238,7 @@ static void resetGraph(tgraph * g, int ncnt, int ecnt)

 #define PQVTYPE float

 #define PQ_TYPES

-#include <fPQ.h>

+#include "fPQ.h"

 #undef PQ_TYPES

 typedef struct {

@@ -1251,7 +1251,7 @@ typedef struct {

 #define N_IDX(pq,n) ((PPQ*)pq)->idxs[n]

 #define PQ_CODE

-#include <fPQ.h>

+#include "fPQ.h"

 #undef PQ_CODE

 #define N_DAD(n) dad[n]

@@ -14,8 +14,8 @@

 #ifndef MULTISPLINE_H

 #define MULTISPLINE_H

-#include <render.h>

-#include <pathutil.h>

+#include "render.h"

+#include "pathutil.h"

 typedef struct router_s router_t;

@@ -26,7 +26,7 @@ extern double drand48(void);

 #endif

 #ifdef ORTHO

-#include <ortho.h>

+#include "ortho.h"

 #endif

 extern void printvis(vconfig_t * cp);

@@ -12,7 +12,7 @@

  *************************************************************************/

 #include <stdio.h>

-#include <vis.h>

+#include "vis.h"

 typedef Ppoint_t point;

@@ -35,7 +35,7 @@

 #include <assert.h>

 #include "matrix_ops.h"

 #include "kkutils.h"

-#include <csolve_VPSC.h>

+#include "csolve_VPSC.h"

 #include "quad_prog_vpsc.h"

 #include "quad_prog_solver.h"

@@ -17,8 +17,8 @@

 #include "config.h"

 #endif

-#include <fPQ.h>

-#include <memory.h>

+#include "fPQ.h"

+#include "memory.h"

 #include <assert.h>

 static snode**  pq;

@@ -13,7 +13,7 @@

 /* Priority Queue Code for shortest path in graph */

-#include <sgraph.h>

+#include "sgraph.h"

 /* typedef snode** PQ; */

 #define N_VAL(n) (n)->n_val

@@ -16,8 +16,8 @@

 #endif

 #include <stddef.h>

-#include <intset.h>

-#include <memory.h>

+#include "intset.h"

+#include "memory.h"

 static Void_t*

 mkIntItem(Dt_t* d,intitem* obj,Dtdisc_t* disc)

@@ -14,7 +14,7 @@

 #ifndef INTSET_H

 #define INTSET_H

-#include <cdt.h>

+#include "cdt.h"

 typedef struct {

     int       id;

@@ -19,10 +19,10 @@

 #define DEBUG

 #include <stddef.h>

-#include <maze.h>

-#include <partition.h>

-#include <memory.h>

-#include <arith.h>

+#include "maze.h"

+#include "partition.h"

+#include "memory.h"

+#include "arith.h"

 /* #include <values.h> */

 #define MARGIN 36;

@@ -14,7 +14,7 @@

 #ifndef MAZE_H

 #define MAZE_H

-#include <sgraph.h>

+#include "sgraph.h"

 enum {M_RIGHT=0, M_TOP, M_LEFT, M_BOTTOM};

@@ -28,7 +28,7 @@

 #define DEBUG

 #include <stddef.h>

-#include <maze.h>

+#include "maze.h"

 #include "fPQ.h"

 #include "memory.h"

 #include "geomprocs.h"

@@ -512,7 +512,7 @@ addNodeEdges (sgraph* sg, cell* cp, snode* np)

 #ifdef DEBUG

-#include <intset.h>

+#include "intset.h"

 static char* bendToStr (bend b)

 {

   char* s;

@@ -1362,7 +1362,7 @@ orthoEdges (Agraph_t* g, int doLbls)

 }

 #ifdef DEBUG

-#include <arith.h>

+#include "arith.h"

 /* #include <values.h> */

 #define TRANS 10

@@ -13,7 +13,7 @@

 #ifndef ORTHO_H

 #define ORTHO_H

-#include <render.h>

+#include "render.h"

 void orthoEdges (Agraph_t* g, int useLbls);

 #endif

@@ -15,9 +15,9 @@

 #include "config.h"

 #endif

-#include <partition.h>

-#include <trap.h>

-#include <memory.h>

+#include "partition.h"

+#include "trap.h"

+#include "memory.h"

 #include <math.h>

 #include <stdlib.h>

@@ -14,7 +14,7 @@

 #ifndef PARTITION_H

 #define PARTITION_H

-#include <maze.h>

+#include "maze.h"

 extern boxf* partition (cell*, int, int*, boxf);

@@ -14,7 +14,7 @@

 #ifndef RAWGRAPH_H

 #define RAWGRAPH_H

-#include <cdt.h>

+#include "cdt.h"

 typedef struct {

   int color;

@@ -21,10 +21,10 @@

 #include <stdio.h>

 #define __USE_ISOC99

 #include <math.h>

-#include <geom.h>

-#include <logic.h>

-#include <memory.h>

-#include <trap.h>

+#include "geom.h"

+#include "logic.h"

+#include "memory.h"

+#include "trap.h"

 #ifdef WIN32

 #define log2(x)  (log(x)/log(2))

@@ -13,8 +13,8 @@

 #include <stdio.h>

 #include <stdlib.h>

-#include <patchwork.h>

-#include <tree_map.h>

+#include "patchwork.h"

+#include "tree_map.h"

 #include "render.h"

 typedef struct treenode_t treenode_t;

@@ -14,7 +14,7 @@

 #ifndef TREE_MAP_H

 #define TREE_MAP_H

-#include <SparseMatrix.h>

+#include "SparseMatrix.h"

 typedef struct rectangle_struct {

   real x[2];/* center */

@@ -16,7 +16,7 @@ extern "C" {

 #endif

-#include <pathgeom.h>

+#include "pathgeom.h"

     void Ptriangulate(Ppoly_t * polygon,

 		      void (*fn) (void *closure, Ppoint_t tri[]),

 		      void *vc);

@@ -16,7 +16,7 @@

 #ifndef _VIS_INCLUDE

 #define _VIS_INCLUDE

-#include <pathgeom.h>

+#include "pathgeom.h"

 #ifdef __cplusplus

 extern "C" {

@@ -22,16 +22,16 @@

 #include <values.h>

 #endif

 #endif

-#include <sfdp.h>

-#include <neato.h>

-#include <adjust.h>

-#include <pack.h>

+#include "sfdp.h"

+#include "neato.h"

+#include "adjust.h"

+#include "pack.h"

 #include <assert.h>

 #include <ctype.h>

-#include <spring_electrical.h>

-#include <overlap.h>

-#include <uniform_stress.h>

-#include <stress_model.h>

+#include "spring_electrical.h"

+#include "overlap.h"

+#include "uniform_stress.h"

+#include "stress_model.h"

 static void sfdp_init_edge(edge_t * e)

 {

@@ -14,7 +14,7 @@

 #ifndef SFDPINTERNAL_H

 #define SFDPINTERNAL_H

-#include <sfdp.h>

+#include "sfdp.h"

 #endif

@@ -14,7 +14,7 @@

 #ifndef SPRING_ELECTRICAL_H

 #define SPRING_ELECTRICAL_H

-#include <SparseMatrix.h>

+#include "SparseMatrix.h"

 enum {ERROR_NOT_SQUARE_MATRIX = -100};

@@ -13,7 +13,7 @@

 #ifndef SPARSEMATRIX_H

 #define  SPARSEMATRIX_H

-#include <general.h>

+#include "general.h"

 #include <stdio.h>

 #define SYMMETRY_EPSILON 0.0000001

@@ -24,9 +24,9 @@

  * In particular, note that Verbose is declared but undefined.

  */

 #ifndef STANDALONE

-#include <logic.h>

-#include <arith.h>

-#include <memory.h>

+#include "logic.h"

+#include "arith.h"

+#include "memory.h"

 #endif

 #define real double

@@ -17,10 +17,10 @@

 #include <iostream>

-#include <variable.h>

-#include <constraint.h>

-#include <generate-constraints.h>

-#include <solve_VPSC.h>

+#include "variable.h"

+#include "constraint.h"

+#include "generate-constraints.h"

+#include "solve_VPSC.h"

 #include <cstdlib>

 #include <cassert>

 #include "csolve_VPSC.h"

@@ -11,7 +11,7 @@

  * Contributors: See CVS logs. Details at http://www.graphviz.org/

  *************************************************************************/

-#include <xdot.h>

+#include "xdot.h"

 #include <stdlib.h>

 #include <string.h>

 #include <ctype.h>